I remember this episode because I don't think Seven's catsuit had ever been tighter than it was in Scientific Method. Bit of a weird and somewhat perverted memory but yeah, the episode was entertaining in other ways too.
My own guess would be that Torres probably would be no. 4, after that it gets a little more difficult. Let's not forget Carey, also a Lieutenant. Torres must have managed to get rid of this competitor shortly after State of Flux - my guess is she kept him in the transport buffer of the transporter unnoticed till Friendship one using the same technique that preserved Sotty for 75 years. Then, there's the EMH, which is an interesting case. I think Voyager' s original CMO (the one that died in Caretaker) would have been fairly high up in that chain of command- my guess would be immediately before or after the Chief Engineer.. The question is though whether that's by rank or by office. My guess would be office is important, otherwise we could never explain Kim being in that hierarchy as a lowly ensign. But, rank must be important too, since the EMH isn't even a commissioned Starfleet officer and as such has no rank and no place in the chain of command.
But technically, the CMO DOES have the authority to relieve someone of duty, and no one (not even Janeway) can relieve him. It is reasonable to assume that this authority devolves on the EMH. And Janeway was definitely medically unfit to command.
The specific ability to relieve Janeway of command for medical reasons, yes. That's established early on, I think in Persistence of Vision. However, I don't think the 'chain of command' authority that probably rested with the original CMO, allowing him to take over if all higher ranking officers were incapacitated, transferred to him on the CMO's death. After all, he has no Starfleet training, and isn't programmed for it (at least, not until the Emergency Command Hologram stuff started). Also, the scene in Persistence of Vision could be read as Janeway humoring the EMH. In Year of Hell, Janeway seems to make short shrift with the EMH trying to assert his medical authority, when business got serious.
But that was illegal. Had the event actually happened (spoiler alert, it didn't), Janeway could have been court martialed for it, especially if the ship was damaged or lives were lost afterward. It could be argued that Janeway was mentally compromised, refused to follow her physician's instructions, and the people who died were her fault.
In the context of the episode, it did happen, it just was undone at the end. Somehow, I have the feeling that in real emergency situations like those, even the knowledge that a court martial would follow wouldn't stop Janeway, without her being needing to be particularly mentally compromised for that. It seems more a matter of circumstances pushing her wrong buttons.